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KamilSJaron / smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data
Apache License 2.0
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Error in estimate_1n_coverage_1d_subsets(total_pair_cov, minor_variant_rel_cov) #143

Closed ferrojm closed 6 months ago

ferrojm commented 6 months ago

Hi, Kamil!

I had this issue when trying to generate the plot :

Error in estimate_1n_coverage_1d_subsets(total_pair_cov, minor_variant_rel_cov) :
  unused argument (minor_variant_rel_cov)

The inputs were created with KMC k=21 (not the tbenavi1/KMC version), using as coverage range L=24 and U=3800 (values obtained with smudgeplot.py cutoff). I am running the conda version (v.0.2.5).

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UPDATE

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Following your comments on other issues, I counted kmers with FastK, but I also got stuck when using smudgeplot.py Although being another issue not realeted to this one, for not creating hundreds of different posts here it goes!

My commands:

FastK -v -t4 -k21 -T6 reads.fastq.gz -NSMUDGEPLOT -Ptemp/ smudgeplot.py hetkmers -o SMUDGEPLOT_k21_pairs SMUDGEPLOT.ktab

and the error:

image

Thanks!

KamilSJaron commented 6 months ago

Hi, you got to install the version in sploidyplot branch: https://github.com/KamilSJaron/smudgeplot/tree/sploidyplot

Sorry about the long silence, I am now in the middle of debugging it before the release and that's going to solve most of these problems people have now.

ferrojm commented 6 months ago

Thanks a lot, Kamil!